Published in Proteins on May 15, 2004
A protein domain-based interactome network for C. elegans early embryogenesis. Cell (2008) 2.23
PSI-2: structural genomics to cover protein domain family space. Structure (2009) 1.92
Predicting transmembrane beta-barrels in proteomes. Nucleic Acids Res (2004) 1.83
Modeling the evolution of protein domain architectures using maximum parsimony. J Mol Biol (2006) 1.53
Progress towards mapping the universe of protein folds. Genome Biol (2004) 1.41
Huntingtin facilitates polycomb repressive complex 2. Hum Mol Genet (2009) 1.32
Evolutionary conservation of domain-domain interactions. Genome Biol (2006) 1.31
Sequence-based prediction of protein domains. Nucleic Acids Res (2004) 1.21
Natively unstructured loops differ from other loops. PLoS Comput Biol (2007) 1.19
Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space. Nucleic Acids Res (2006) 1.17
Structural genomics target selection for the New York consortium on membrane protein structure. J Struct Funct Genomics (2009) 1.14
Domain mobility in proteins: functional and evolutionary implications. Brief Bioinform (2009) 1.11
ThreaDom: extracting protein domain boundary information from multiple threading alignments. Bioinformatics (2013) 1.05
NMPdb: Database of Nuclear Matrix Proteins. Nucleic Acids Res (2005) 0.98
CHOP: parsing proteins into structural domains. Nucleic Acids Res (2004) 0.98
Physical protein-protein interactions predicted from microarrays. Bioinformatics (2008) 0.94
This Déjà vu feeling--analysis of multidomain protein evolution in eukaryotic genomes. PLoS Comput Biol (2012) 0.89
FIEFDom: a transparent domain boundary recognition system using a fuzzy mean operator. Nucleic Acids Res (2008) 0.87
The accurate assessment of small-angle X-ray scattering data. Acta Crystallogr D Biol Crystallogr (2015) 0.86
Predicted Molecular Effects of Sequence Variants Link to System Level of Disease. PLoS Comput Biol (2016) 0.79
Protein domain boundary predictions: a structural biology perspective. Open Biochem J (2009) 0.75
SNAP predicts effect of mutations on protein function. Bioinformatics (2008) 15.39
SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res (2007) 8.46
Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins (2002) 5.29
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
A mutation in VPS35, encoding a subunit of the retromer complex, causes late-onset Parkinson disease. Am J Hum Genet (2011) 4.52
Critical assessment of methods of protein structure prediction-Round VII. Proteins (2007) 3.23
Mimicking cellular sorting improves prediction of subcellular localization. J Mol Biol (2005) 3.21
Three-dimensional structures of membrane proteins from genomic sequencing. Cell (2012) 3.02
Analysing six types of protein-protein interfaces. J Mol Biol (2003) 2.96
Critical assessment of methods of protein structure prediction (CASP)--round 6. Proteins (2005) 2.58
Alignments grow, secondary structure prediction improves. Proteins (2002) 2.56
EVA: Evaluation of protein structure prediction servers. Nucleic Acids Res (2003) 2.50
Reliability of assessment of protein structure prediction methods. Structure (2002) 2.39
Sequence conserved for subcellular localization. Protein Sci (2002) 2.36
Automatic target selection for structural genomics on eukaryotes. Proteins (2004) 2.34
Outcome of a workshop on archiving structural models of biological macromolecules. Structure (2006) 2.32
The protein target list of the Northeast Structural Genomics Consortium. Proteins (2004) 2.31
Transmembrane helix predictions revisited. Protein Sci (2002) 2.28
Critical assessment of methods of protein structure prediction - Round VIII. Proteins (2009) 2.25
Protein-protein interaction hotspots carved into sequences. PLoS Comput Biol (2007) 2.15
PROFbval: predict flexible and rigid residues in proteins. Bioinformatics (2006) 2.04
Domains, motifs and clusters in the protein universe. Curr Opin Chem Biol (2003) 2.02
Predicted protein-protein interaction sites from local sequence information. FEBS Lett (2003) 2.00
Loopy proteins appear conserved in evolution. J Mol Biol (2002) 1.96
PSI-2: structural genomics to cover protein domain family space. Structure (2009) 1.92
Protein names precisely peeled off free text. Bioinformatics (2004) 1.87
Predicting transmembrane beta-barrels in proteomes. Nucleic Acids Res (2004) 1.83
Distinguishing protein-coding from non-coding RNAs through support vector machines. PLoS Genet (2006) 1.81
NLSdb: database of nuclear localization signals. Nucleic Acids Res (2003) 1.81
PROFcon: novel prediction of long-range contacts. Bioinformatics (2005) 1.81
UniqueProt: Creating representative protein sequence sets. Nucleic Acids Res (2003) 1.78
Understanding the physical properties that control protein crystallization by analysis of large-scale experimental data. Nat Biotechnol (2009) 1.78
Comprehensive in silico mutagenesis highlights functionally important residues in proteins. Bioinformatics (2008) 1.74
Prediction of DNA-binding residues from sequence. Bioinformatics (2007) 1.72
ISIS: interaction sites identified from sequence. Bioinformatics (2007) 1.71
Epitome: database of structure-inferred antigenic epitopes. Nucleic Acids Res (2006) 1.70
Improved disorder prediction by combination of orthogonal approaches. PLoS One (2009) 1.63
Continuum secondary structure captures protein flexibility. Structure (2002) 1.63
Better prediction of sub-cellular localization by combining evolutionary and structural information. Proteins (2003) 1.61
Protein-protein interactions more conserved within species than across species. PLoS Comput Biol (2006) 1.61
Protein flexibility and rigidity predicted from sequence. Proteins (2005) 1.58
NORSp: Predictions of long regions without regular secondary structure. Nucleic Acids Res (2003) 1.58
Novel leverage of structural genomics. Nat Biotechnol (2007) 1.57
Inferring sub-cellular localization through automated lexical analysis. Bioinformatics (2002) 1.55
Structural genomics is the largest contributor of novel structural leverage. J Struct Funct Genomics (2009) 1.52
Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery. Drug Discov Today (2005) 1.46
Natively unstructured regions in proteins identified from contact predictions. Bioinformatics (2007) 1.45
PEP: Predictions for Entire Proteomes. Nucleic Acids Res (2003) 1.39
CASP6 assessment of contact prediction. Proteins (2005) 1.39
Protein disorder--a breakthrough invention of evolution? Curr Opin Struct Biol (2011) 1.37
Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks. Proteins (2006) 1.35
Target space for structural genomics revisited. Bioinformatics (2002) 1.32
Solution NMR structure of the NlpC/P60 domain of lipoprotein Spr from Escherichia coli: structural evidence for a novel cysteine peptidase catalytic triad. Biochemistry (2008) 1.27
Crystal structure of a potassium ion transporter, TrkH. Nature (2011) 1.25
Homologue structure of the SLAC1 anion channel for closing stomata in leaves. Nature (2010) 1.22
Sequence-based prediction of protein domains. Nucleic Acids Res (2004) 1.21
DSSPcont: Continuous secondary structure assignments for proteins. Nucleic Acids Res (2003) 1.20
Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination. J Am Chem Soc (2005) 1.19
Natively unstructured loops differ from other loops. PLoS Comput Biol (2007) 1.19
LOC3D: annotate sub-cellular localization for protein structures. Nucleic Acids Res (2003) 1.18
Membrane protein prediction methods. Methods (2007) 1.17
SNPdbe: constructing an nsSNP functional impacts database. Bioinformatics (2011) 1.16
Better prediction of functional effects for sequence variants. BMC Genomics (2015) 1.16
MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence. Bioinformatics (2008) 1.15
Structural genomics target selection for the New York consortium on membrane protein structure. J Struct Funct Genomics (2009) 1.14
LOCnet and LOCtarget: sub-cellular localization for structural genomics targets. Nucleic Acids Res (2004) 1.12
LocTree2 predicts localization for all domains of life. Bioinformatics (2012) 1.11
State-of-the-art in membrane protein prediction. Appl Bioinformatics (2002) 1.11
Protein subcellular localization prediction using artificial intelligence technology. Methods Mol Biol (2008) 1.09
Improving fold recognition without folds. J Mol Biol (2004) 1.09
News from the protein mutability landscape. J Mol Biol (2013) 1.08
The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins. J Struct Funct Genomics (2010) 1.07
Automated identification of complementarity determining regions (CDRs) reveals peculiar characteristics of CDRs and B cell epitopes. J Immunol (2008) 1.05
Crystal structure of a phosphorylation-coupled saccharide transporter. Nature (2011) 1.05
Coordinating the impact of structural genomics on the human α-helical transmembrane proteome. Nat Struct Mol Biol (2013) 1.05
Static benchmarking of membrane helix predictions. Nucleic Acids Res (2003) 1.05
Protein folding rates estimated from contact predictions. J Mol Biol (2005) 1.03
NLProt: extracting protein names and sequences from papers. Nucleic Acids Res (2004) 1.02
Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference. BMC Bioinformatics (2011) 1.02
Secondary structure assignment. Methods Biochem Anal (2003) 1.02
Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome. J Proteome Res (2009) 1.02
PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. Nucleic Acids Res (2006) 1.01
Structural genomics plucks high-hanging membrane proteins. Curr Opin Struct Biol (2012) 0.98
Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be. Bioinformatics (2010) 0.98
NMPdb: Database of Nuclear Matrix Proteins. Nucleic Acids Res (2005) 0.98
CHOP: parsing proteins into structural domains. Nucleic Acids Res (2004) 0.98
Correlating protein function and stability through the analysis of single amino acid substitutions. BMC Bioinformatics (2009) 0.97
Structural elucidation of the Cys-His-Glu-Asn proteolytic relay in the secreted CHAP domain enzyme from the human pathogen Staphylococcus saprophyticus. Proteins (2009) 0.97
Cataloging proteins in cell cycle control. Methods Mol Biol (2004) 0.96
ISCB computational biology Wikipedia competition. PLoS Comput Biol (2013) 0.96
In silico mutagenesis: a case study of the melanocortin 4 receptor. FASEB J (2009) 0.96
Disease-related mutations predicted to impact protein function. BMC Genomics (2012) 0.96
MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data. Nucleic Acids Res (2010) 0.96
CAFASP3 in the spotlight of EVA. Proteins (2003) 0.95
Physical protein-protein interactions predicted from microarrays. Bioinformatics (2008) 0.94
ISCB Public Policy Statement on Open Access to Scientific and Technical Research Literature. PLoS Comput Biol (2011) 0.93
ISCB public policy statement on open access to scientific and technical research literature. Bioinformatics (2011) 0.93
Structural basis of O6-alkylguanine recognition by a bacterial alkyltransferase-like DNA repair protein. J Biol Chem (2010) 0.92
Transmembrane domains in the functions of Fc receptors. Biophys Chem (2003) 0.92
Structural genomics reveals EVE as a new ASCH/PUA-related domain. Proteins (2009) 0.92